Merge pull request #2 from tractometry/no_yeatmanlab

Replace yeatmanlab with tractometry wherever that appears.

.github/CONTRIBUTING.md

@@ -94,19 +94,19 @@ is difficult to be described as one unit of work, please consider splitting it i
 
 The current list of issue labels are [here][link_labels] and include:
 
-* [![Good first issue](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/good%20first%20issue)][link_firstissue] *These issues contain a task that is amenable to new contributors because it doesn't entail a steep learning curve.*
+* [![Good first issue](https://img.shields.io/github/labels/tractometry/pyAFQ/good%20first%20issue)][link_firstissue] *These issues contain a task that is amenable to new contributors because it doesn't entail a steep learning curve.*
 
     If you feel that you can contribute to one of these issues,
     we especially encourage you to do so!
 
-* [![Bug](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/bug)][link_bugs] *These issues point to problems in the project.*
+* [![Bug](https://img.shields.io/github/labels/tractometry/pyAFQ/bug)][link_bugs] *These issues point to problems in the project.*
 
     If you find new a bug, please give as much detail as possible in your issue,
     including steps to recreate the error.
     If you experience the same bug as one already listed,
     please add any additional information that you have as a comment.
 
-* [![Enhancement](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/enhancement)][link_enhancement] *These issues are asking for new features and improvements to be considered by the project.*
+* [![Enhancement](https://img.shields.io/github/labels/tractometry/pyAFQ/enhancement)][link_enhancement] *These issues are asking for new features and improvements to be considered by the project.*
 
     Please try to make sure that your requested feature is distinct from any others
     that have already been requested or implemented.
@@ -118,16 +118,16 @@ we have two sets of special labels:
 
 | Label                                                                                           | Description                                                                                           |
 |--------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------|
-| ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20low)    | Estimation of the downstream impact the proposed feature/bugfix will have.                |
-| ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20low)    | Estimation of effort required to implement the requested feature or fix the reported bug. |
+| ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20low)    | Estimation of the downstream impact the proposed feature/bugfix will have.                |
+| ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20low)    | Estimation of effort required to implement the requested feature or fix the reported bug. |
 
 These labels help triage and set priorities to the development tasks.
 For instance, one bug regression that has been reported to affect most of the users after
 a release with an easy fix because it is a known old problem that came back.
-Such an issue will typically be assigned the following labels ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/bug) ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20high) ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20low), and its priority will be maximal since addressing low-effort high-impact deliver the maximum turnout without increasing the churn by much.
+Such an issue will typically be assigned the following labels ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/bug) ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20high) ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20low), and its priority will be maximal since addressing low-effort high-impact deliver the maximum turnout without increasing the churn by much.
 
-Of course, the implementation of long-term goaled lines may include the scheduling of ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20medium) ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20high).
-Finally, ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/impact%3A%20low) ![GitHub labels](https://img.shields.io/github/labels/yeatmanlab/pyAFQ/effort%3A%20high) issues are less likely to be addressed.
+Of course, the implementation of long-term goaled lines may include the scheduling of ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20medium) ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20high).
+Finally, ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/impact%3A%20low) ![GitHub labels](https://img.shields.io/github/labels/tractometry/pyAFQ/effort%3A%20high) issues are less likely to be addressed.
 
 ## Making a change
 
@@ -156,7 +156,7 @@ but those accepted fastest will follow a workflow similar to the following:
   add the ["upstream" pyAFQ repository as a remote][link_addremote]
   to your locally cloned repository.
     ```Shell
-    git remote add upstream https://github.com/yeatmanlab/pyAFQ.git
+    git remote add upstream https://github.com/tractometry/pyAFQ.git
     ```
     Make sure to [keep your fork up to date][link_updateupstreamwiki] with the upstream repository.<br />
     For example, to update your master branch on your local cloned repository:
@@ -240,7 +240,7 @@ acknowledge that any contributions will be licensed under the same terms.
     [MetPy project](https://github.com/Unidata/MetPy).
 
 [link_github]: https://github.com/
-[link_pyAFQ]: https://github.com/yeatmanlab/pyAFQ
+[link_pyAFQ]: https://github.com/tractometry/pyAFQ
 [link_signupinstructions]: https://help.github.com/articles/signing-up-for-a-new-github-account
 
 [link_neurostars]: https://neurostars.org/tags/pyAFQ
@@ -254,13 +254,13 @@ acknowledge that any contributions will be licensed under the same terms.
 [rick_roll]: https://www.youtube.com/watch?v=dQw4w9WgXcQ
 
 [autofq]: https://autofq.org/
-[link_issues]: https://github.com/yeatmanlab/pyAFQ/issues
-[link_labels]: https://github.com/yeatmanlab/pyAFQ/labels
+[link_issues]: https://github.com/tractometry/pyAFQ/issues
+[link_labels]: https://github.com/tractometry/pyAFQ/labels
 [link_discussingissues]: https://help.github.com/articles/discussing-projects-in-issues-and-pull-requests
 
-[link_bugs]: https://github.com/yeatmanlab/pyAFQ/labels/bug
-[link_firstissue]: https://github.com/yeatmanlab/pyAFQ/labels/good%20first%20issue
-[link_enhancement]: https://github.com/yeatmanlab/pyAFQ/labels/enhancement
+[link_bugs]: https://github.com/tractometry/pyAFQ/labels/bug
+[link_firstissue]: https://github.com/tractometry/pyAFQ/labels/good%20first%20issue
+[link_enhancement]: https://github.com/tractometry/pyAFQ/labels/enhancement
 
 [link_pullrequest]: https://help.github.com/articles/creating-a-pull-request-from-a-fork
 [link_fork]: https://help.github.com/articles/fork-a-repo/

.github/workflows/docbuild.yml

@@ -2,6 +2,13 @@ name: Documentation build
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: write
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -36,8 +43,6 @@ jobs:
         path: docs/build/html
     - name: Publish docs to Github Pages
       if: startsWith(github.event.ref, 'refs/tags')
-      uses: JamesIves/github-pages-deploy-action@releases/v3
+      uses: JamesIves/github-pages-deploy-action@releases/v4
       with:
-        ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }}
-        BRANCH: gh-pages # The branch the action should deploy to.
-        FOLDER: docs/build/html # The folder the action should deploy.
+        folder: docs/build/html

.github/workflows/docker_pyafq.yml

@@ -35,7 +35,7 @@ jobs:
         sh ./gpu_docker/docker-build.sh \
           "${GITHUB_REF:10}" "nrdg" "11.4.3-devel-ubuntu20.04" "11"
 
-    - name: Login to GHCR 
+    - name: Login to GHCR
       if: github.ref == 'refs/heads/master' || startsWith(github.event.ref, 'refs/tags')
       uses: docker/login-action@v1
       with:

.github/workflows/docker_pyafq_cuda12.yml

@@ -25,9 +25,9 @@ jobs:
         sh ./gpu_docker/docker-build.sh \
           "${GITHUB_REF:10}" "nrdg" "12.0.1-devel-ubuntu20.04" "12"
 
-    - name: Login to GHCR 
+    - name: Login to GHCR
       if: github.ref == 'refs/heads/master' || startsWith(github.event.ref, 'refs/tags')
-      uses: docker/login-action@v1
+      uses: docker/login-action@v3
       with:
         registry: ghcr.io
         username: nrdg

.github/workflows/test.yml

@@ -2,6 +2,10 @@ name: Test suite
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
 

.zenodo.json

@@ -69,7 +69,7 @@
   "license": "BSD-3-Clause",
   "related_identifiers": [
     {
-      "identifier": "http://yeatmanlab.github.io/pyAFQ",
+      "identifier": "http://tractometry.org/pyAFQ",
       "relation": "isPartOf",
       "scheme": "url"
     }

AFQ/data/fetch.py

@@ -203,7 +203,7 @@ def read_callosum_templates(as_img=True, resample_to=False):
 #
 # - atlas: https://www.nitrc.org/projects/pediatricatlas
 #
-# - pediatric templates: https://github.com/yeatmanlab/AFQ/tree/babyAFQ
+# - pediatric templates: https://github.com/tractometry/AFQ/tree/babyAFQ
 #
 # Templates downloaded from:
 #

AFQ/tasks/viz.py

@@ -404,7 +404,7 @@ def init_viz_backend(viz_backend_spec="plotly_no_gif",
     viz_backend_spec : str, optional
         Which visualization backend to use.
         See Visualization Backends page in documentation for details:
-        https://yeatmanlab.github.io/pyAFQ/usage/viz_backend.html
+        https://tractometry.org/pyAFQ/usage/viz_backend.html
         One of {"fury", "plotly", "plotly_no_gif"}.
         Default: "plotly_no_gif"
     """

README.md

@@ -1,7 +1,7 @@
 # pyAFQ
 Automated Fiber Quantification ... in Python.
 
-For details, see [Documentation](https://yeatmanlab.github.io/pyAFQ)
+For details, see [Documentation](https://tractometry.org/pyAFQ)
 
 For further analysis of results, see [AFQ-Insight](https://github.com/richford/AFQ-Insight)
 

bin/pyAFQ

@@ -23,7 +23,7 @@ usage = \
 Runs full AFQ processing as specified in the configuration file.
 
 For details about configuration, see instructions in:
-https://yeatmanlab.github.io/pyAFQ/usage/config.html
+https://tractometry.org/pyAFQ/usage/config.html
 
 The default configuration file looks like:
 
@@ -104,7 +104,7 @@ def parse_cli(arg_dict):
         logger.info(
             "Your use of pyAFQ is being recorded using Google Analytics. "
             "For more information, please refer to the pyAFQ documentation: "
-            "https://yeatmanlab.github.io/pyAFQ/usage.html#usage-tracking-with-google-analytics. "  # noqa
+            "https://tractometry.org/pyAFQ/usage.html#usage-tracking-with-google-analytics. "  # noqa
             "To turn this off, use the `--notrack` "
             "flag when using the pyAFQ CLI")
         import popylar

docs/Makefile

@@ -20,7 +20,7 @@ help:
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 upload: html
-		./upload-gh-pages.sh build/html/ pyAFQ yeatmanlab
+		./upload-gh-pages.sh build/html/ pyAFQ tractometry
 
 .PHONY: distclean realclean
 

docs/source/conf.py

@@ -110,7 +110,7 @@
     "icon_links": [
         {
             "name": "GitHub",
-            "url": "https://github.com/yeatmanlab/pyAFQ",
+            "url": "https://github.com/tractometry/pyAFQ",
             "icon": "fab fa-github-square",
         }]
 
@@ -122,7 +122,7 @@
 
 html_context = {
     "github_url": "https://github.com",
-    "github_user": "yeatmanlab",
+    "github_user": "tractometry",
     "github_repo": "pyAFQ",
     "github_version": "master",
     "doc_path": "docs/source",

docs/source/explanations/modeling.rst

@@ -11,7 +11,7 @@ For an interesting perspective on modeling of tissue properties from diffusion
 MRI data, please refer to a recent paper by Novikov and colleagues
 [Novikov2018]_.
 
-`This page <https://yeatmanlab.github.io/pyAFQ/reference/methods.rst>` includes
+`This page <https://tractometry.org/pyAFQ/reference/methods.rst>` includes
 a list of the model parameters that are accessible through the
 :class:`AFQ.api.group.GroupAFQ` and :class:`AFQ.api.participant.ParticipantAFQ`
 objects.

docs/source/howto/contributing.rst

@@ -4,9 +4,9 @@ How to contribute to pyAFQ
 ~~~~~~~~~~~~~~~~~~~~~
 
 pyAFQ is an open-source software project. This means that you are welcome
-to use it (see `LICENSE <https://github.com/yeatmanlab/pyAFQ/blob/master/LICENSE>`_ for details).
+to use it (see `LICENSE <https://github.com/tractometry/pyAFQ/blob/master/LICENSE>`_ for details).
 
 It also means that we welcome contributions from developers outside of our
 research collaboration and we will credit these contributions appropriately.
 
-Detailed guidelines for contribution are available `here <https://github.com/yeatmanlab/pyAFQ/blob/master/.github/CONTRIBUTING.md>`_.
+Detailed guidelines for contribution are available `here <https://github.com/tractometry/pyAFQ/blob/master/.github/CONTRIBUTING.md>`_.

docs/source/howto/developing/index.rst

@@ -3,7 +3,7 @@ How to develop `pyAFQ`
 
 We are glad that you are here! That probably means that you are interested in contributing to the development of `pyAFQ`.
 Before you continue reading specific topics below, please read the contribution guidelines
-`here <https://github.com/yeatmanlab/pyAFQ/blob/master/.github/CONTRIBUTING.md>`_ .
+`here <https://github.com/tractometry/pyAFQ/blob/master/.github/CONTRIBUTING.md>`_ .
 
 As an overview, the pyAFQ code can roughly be divided into 5 sections.
 
@@ -20,14 +20,14 @@ As an overview, the pyAFQ code can roughly be divided into 5 sections.
 3 - Code which describes tasks within the tractometry workflow.
     **For most contributors, this is a good place to start**. The user-facing API/CLI
     use a workflow automatically constructed from these discrete tasks,
-    as described in `tasks <https://yeatmanlab.github.io/pyAFQ/developing/tasks.html>`_ .
+    as described in `tasks <https://tractometry.org/pyAFQ/developing/tasks.html>`_ .
     For shorter tasks, one may only need to edit the relevant task file.
     For longer tasks, one can add to the files containing low-level
     functionality.
 
 4 - Code which describes 'definitions', classes which help users describe
     inputs to pyAFQ. These have particular requirements and must be
-    BIDS compatible, see `here <https://yeatmanlab.github.io/pyAFQ/developing/definitions.html>`_ .
+    BIDS compatible, see `here <https://tractometry.org/pyAFQ/developing/definitions.html>`_ .
 
 5 - Code which contains tests, such as in the tests folder and utils/tests.
     It is important when adding new functionality to add a corresponding test.

docs/source/howto/developing/releasing.rst

@@ -3,7 +3,7 @@ How to create a release
 
 The current release process entails the following steps:
 
-#. Make sure you have the `master` branch locally updated to the state on the `main fork of the project <https://github.com/yeatmanlab/pyAFQ/tree/master>`_.
+#. Make sure you have the `master` branch locally updated to the state on the `main fork of the project <https://github.com/tractometry/pyAFQ/tree/master>`_.
 
 #. Update CHANGES.rst: run the script `.maintenance/update_changes.sh <next_tag>`, with the tag set to the version string of the upcoming release. Further edit the notes to add a short summary at the top.
 
@@ -18,8 +18,8 @@ The current release process entails the following steps:
     git push upstream 0.5
 
 #. On GitHub:
-    - Navigate to the `"Releases" tab <https://github.com/yeatmanlab/pyAFQ/releases>`_
-    - Click on `"Draft a new release" <https://github.com/yeatmanlab/pyAFQ/releases/new>`_.
+    - Navigate to the `"Releases" tab <https://github.com/tractometry/pyAFQ/releases>`_
+    - Click on `"Draft a new release" <https://github.com/tractometry/pyAFQ/releases/new>`_.
     - In the "Tag version" box enter the version string of this release.
     - In "Release title" enter (for example) "Version 0.5".
     - In the description box copy the entry in CHANGES.rst corresponding to this release (with the exclusion of the title).

docs/source/howto/getting_help.rst

@@ -6,7 +6,7 @@ one of the following communication channels:
 
 #. If you encounter a problem using the code, you can post an issue on our
    GitHub repository by going to this
-   `page <https://github.com/yeatmanlab/pyAFQ/issues>`_ and clicking on the "new
+   `page <https://github.com/tractometry/pyAFQ/issues>`_ and clicking on the "new
    issue" button. Please provide all pertinent information about the issue you
    are facing: we often need to know what version of the software you are
    running and how you installed it, as well as the operating system that you
@@ -17,7 +17,7 @@ one of the following communication channels:
 
 #. If you would like to start a discussion about future developments or about
    the method, consider starting a discussion on this
-   `page <https://github.com/yeatmanlab/pyAFQ/discussions>`_.
+   `page <https://github.com/tractometry/pyAFQ/discussions>`_.
 
 #. Questions regarding the method and its use can also be posted to the
    `Neurostars <https://neurostars.org/>`_ Q&A forum.

docs/source/howto/installation_guide.rst

@@ -25,11 +25,11 @@ The development version is probably less stable, but might include new
 features and fixes. There are two ways to install this version. The first
 uses ``pip``::
 
-  pip install git+https://github.com/yeatmanlab/pyAFQ.git
+  pip install git+https://github.com/tractometry/pyAFQ.git
 
 The other requires that you clone the source code to your machine::
 
-  git clone https://github.com/yeatmanlab/pyAFQ.git
+  git clone https://github.com/tractometry/pyAFQ.git
 
 With both installation methods, you can include extensions to the base installation in square brackets. Change your working directory into the top-level directory of this repo
 and issue::

docs/source/howto/usage/docker.rst

@@ -2,7 +2,7 @@ The pyAFQ docker image
 ~~~~~~~~~~~~~~~~~~~~~~
 
 Everytime a new commit is made to master the
-`pyAFQ github <https://github.com/yeatmanlab/pyAFQ>`_,
+`pyAFQ github <https://github.com/tractometry/pyAFQ>`_,
 a new image is pushed to the
 `NRDG github <https://github.com/orgs/nrdg/packages/container/package/pyafq>`_.
 This image contains an installation of the latest version of

docs/source/howto/usage/kwargs.rst

@@ -108,7 +108,7 @@ brain_mask_definition: instance from `AFQ.definitions.image`, optional
 bundle_info: strings, dict, or BundleDict, optional
 	List of bundle names to include in segmentation,
 	or a bundle dictionary (see BundleDict for inspiration),
-	or a BundleDict. See `Defining Custom Bundle Dictionaries <https://yeatmanlab.github.io/pyAFQ/reference/bundledict.html>`_
+	or a BundleDict. See `Defining Custom Bundle Dictionaries <https://tractometry.org/pyAFQ/reference/bundledict.html>`_
 	in the `usage` section of pyAFQ's documentation for details.
 	If None, will get all appropriate bundles for the chosen
 	segmentation algorithm.
@@ -228,7 +228,7 @@ n_points_indiv: int or None
 viz_backend_spec: str, optional
 	Which visualization backend to use.
 	See Visualization Backends page in documentation for details:
-	https://yeatmanlab.github.io/pyAFQ/usage/viz_backend.html
+	https://tractometry.org/pyAFQ/usage/viz_backend.html
 	One of {"fury", "plotly", "plotly_no_gif"}.
 	Default: "plotly_no_gif"